[go] GO Slims

[Midori Harris]

Hi Rama,

This is timely -- I've exchanged some email over the past few days with 
Darren Natale at PIR on essentially the same subject. They have a slim 
that they would like to have incorporated into GO. I forwarded the initial 
request and some follow-up info to the GO managers for comment. So far, 
Michael and Suzi have said they are happy to have GO add the PIR slim, and 
no one else on the managers' list has commented.

For the time being, I'm inclined to add the slims to the 
gene_ontology_edit.obo file to keep them in sync with the rest of the 
ontology. From what John said in the earlier exchange, it seems it won't 
be very difficult to convert to separate files for slims whenever we see 
fit.

I know that Amelia plans to update the GO slim script in the next week or 
two, so any new slims we add to the gene_ontology_edit.obo file will 
appear in the slim directory. That script can presumably also be adapted 
to find the slims in one or more external files if/when we go that route.

Midori

On Wed, 10 Oct 2007, Rama Balakrishnan wrote:

>
> The topic of adding more GO Slims was slated for discussion at the GOC 
> meeting, but somehow did not happen.  There was a proposal to maintain the 
> slims in a separate file instead of adding categories into the current OBO as 
> we do it now.  But no conclusion was made.
>
> CGD (and others, please see below) would like to make their GO Slims 
> available. Since no conclusion was made, can we proceed using the current 
> system (maintaining categories within the obo file)?
>
> Background:
> Currently we store the various GO slims as categories in the 
> gene_ontology_edit.obo file. I believe there is a script that parses this 
> file and puts each GO slim on the FTP site. This mechanism was put in place 
> to keep the GO slims current with the ontology (to make sure obsolete terms 
> are removed from the GO slims, term merges are represented correctly and so 
> on).
>
>
> A curator from the Candida Genome Database emailed us asking how to post the 
> Candida GO slim that CGD has just developed. I understand Alex from MGI, 
> Michelle from TIGR all have GO slims that they want to add.  There was an 
> email discussion on the GO mailing list about this topic. Here is a link to 
> that thread-
>
> http://genetics.stanford.edu/go-email/email-go/go-arc/go-2007/0451.html
>
> Thanks,
>
> Rama